LAMMPS (28 Mar 2023 - Development)
  using 1 OpenMP thread(s) per MPI task
# 2d rounded polygon bodies

variable    r     index 4
variable    steps index 100000
variable    T     index 0.5
variable    P     index 0.1
variable    seed  index 980411

units       lj
dimension   2

atom_style  body rounded/polygon 1 6
atom_modify map array
read_data   data.squares
Reading data file ...
  orthogonal box = (0 0 -0.5) to (12 12 0.5)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2 atoms
  2 bodies
  read_data CPU = 0.001 seconds

replicate   $r $r 1
replicate   4 $r 1
replicate   4 4 1
Replication is creating a 4x4x1 = 16 times larger system...
  orthogonal box = (0 0 -0.5) to (48 48 0.5)
  1 by 1 by 1 MPI processor grid
  32 atoms
  replicate CPU = 0.001 seconds

velocity    all create $T ${seed} dist gaussian mom yes rot yes
velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity    all create 0.5 980411 dist gaussian mom yes rot yes

variable cut_inner  equal 0.5
variable k_n        equal 100
variable k_na       equal 2
variable c_n        equal 1
variable c_t        equal 1
variable mu         equal 0.1
variable delta_ua   equal 0.5

pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2

comm_modify vel yes

neighbor     0.5 bin
neigh_modify every 1 delay 0 check yes

timestep     0.001

#fix         1 all nve/body
#fix         1 all nvt/body temp $T $T 1.0
fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0              y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0

fix          2 all enforce2d

#compute      1 all body/local id 1 2 3
#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]

thermo_style custom step ke pe etotal press
thermo       1000

#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
#dump_modify  2 pad 6

run          ${steps}
run          100000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.1568542
  ghost atom cutoff = 6.1568542
  binsize = 3.0784271, bins = 16 16 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair body/rounded/polygon, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.386 | 5.386 | 5.386 Mbytes
   Step         KinEng         PotEng         TotEng         Press     
         0   0.484375       0.25           0.734375       0.0067274306 
      1000   0.39720235     0.0015845731   0.39878692     0.00223489   
      2000   0.42893425     0.011718891    0.44065314     0.0027413224 
      3000   0.57823511     0.012407489    0.5906426      0.0025306081 
      4000   0.71610647     0.028149437    0.74425591     0.0016504948 
      5000   0.84027279     0.018917017    0.8591898      0.0037451875 
      6000   0.72410001     0.073495378    0.79759539     0.00018672875
      7000   0.53886484     0.077723366    0.61658821     0.004729216  
      8000   0.66196054     0.05502242     0.71698296     0.0054997323 
      9000   0.93104065     0.071628784    1.0026694      0.011330629  
     10000   0.75494389     0.15204106     0.90698495     0.021702117  
     11000   0.72349154     0.11102332     0.83451486     0.019264158  
     12000   0.56216531     0.117059       0.67922431    -0.028295891  
     13000   0.63793498     0.11701868     0.75495366     0.029470631  
     14000   0.62996509     0.020871971    0.65083706     0.0086224023 
     15000   0.6403927      0.0091092209   0.64950192     0.016897685  
     16000   0.70288045     0.046856749    0.7497372      0.02312871   
     17000   0.6820593      0.038994474    0.72105377     0.0068705173 
     18000   0.75623543     0.0069908315   0.76322626     0.025170959  
     19000   0.85962145     0.059005169    0.91862661     0.012725758  
     20000   0.73334823     0.033043489    0.76639172     0.023661433  
     21000   0.60850654     0.081277767    0.68978431     0.021031136  
     22000   0.38251144     0.27624263     0.65875407     0.047336318  
     23000   0.4288127      0.30632792     0.73514062     0.034108416  
     24000   0.4452138      0.13179024     0.57700404     0.010303821  
     25000   0.48091107     0.1816109      0.66252197     0.021201342  
     26000   0.67970784     0.088616708    0.76832455     0.034997245  
     27000   0.8223642      0.08699442     0.90935862     0.023508839  
     28000   0.60062179     0.1119578      0.71257959    -0.0010008016 
     29000   0.54629437     0.1202995      0.66659387     0.040613547  
     30000   0.28102412     0.38657163     0.66759575    -0.0086538064 
     31000   0.12433474     0.18824131     0.31257605     0.049899211  
     32000   0.089510322    0.20890679     0.29841711     0.045555094  
     33000   0.12657665     0.17720119     0.30377784     0.028306214  
     34000   0.18400652     0.17677189     0.36077841     0.034628531  
     35000   0.24048631     0.11010844     0.35059475     0.029848365  
     36000   0.33435006     0.077341882    0.41169194     0.055963098  
     37000   0.46088842     0.1210638      0.58195222     0.072006022  
     38000   0.76551752     0.07037755     0.83589507     0.018204686  
     39000   0.89388464     0.080990198    0.97487484     0.038361105  
     40000   0.65618718     0.078644754    0.73483193     0.040567246  
     41000   0.47284043     0.16391389     0.63675432     0.027523843  
     42000   0.52454668     0.057988616    0.58253529     0.03122996   
     43000   0.78769394     0.08405077     0.87174471     0.044743697  
     44000   0.92932837     0.093922981    1.0232514      0.042510479  
     45000   0.5722596      0.17607834     0.74833794     0.034646914  
     46000   0.54352389     0.085652886    0.62917677     0.033203865  
     47000   0.45608912     0.25183842     0.70792754     0.08370224   
     48000   0.47530886     0.10106466     0.57637352     0.046113986  
     49000   0.67945305     0.0065249477   0.68597799     0.054743491  
     50000   0.49661922     0.097381596    0.59400082     0.006998965  
     51000   0.60992235     0.059017331    0.66893968     0.09445106   
     52000   0.69563455     0.18702969     0.88266424     0.034154598  
     53000   0.87598532     0.18260917     1.0585945      0.065734536  
     54000   0.58822846     0.27562038     0.86384884     0.0764045    
     55000   0.43454899     0.17174441     0.6062934      0.026434052  
     56000   0.4004495      0.12778644     0.52823594     0.065986005  
     57000   0.36272102     0.09849578     0.4612168      0.064217596  
     58000   0.40987214     0.21777618     0.62764832     0.058625636  
     59000   0.64813089     0.1479689      0.79609979     0.033378701  
     60000   0.90328265     0.11049926     1.0137819      0.055828397  
     61000   0.82921839     0.074638688    0.90385707     0.062488824  
     62000   0.63223087     0.094386302    0.72661718     0.054784559  
     63000   0.62946839     0.087807829    0.71727622     0.058398323  
     64000   0.79784108     0.094756776    0.89259786     0.065765914  
     65000   0.87500942     0.13514078     1.0101502      0.068123475  
     66000   0.66961949     0.19942965     0.86904914     0.065587832  
     67000   0.61612396     0.11436282     0.73048678     0.061233427  
     68000   0.74149449     0.03129016     0.77278465     0.072517897  
     69000   0.84060202     0.027261803    0.86786382     0.063374451  
     70000   0.78182528     0.023528774    0.80535405     0.07431822   
     71000   0.71611101     0.023512727    0.73962374     0.069575276  
     72000   0.68437263     0.023941199    0.70831382     0.069821154  
     73000   0.75652323     0.023580324    0.78010355     0.075046425  
     74000   0.92077658     0.023272419    0.944049       0.070992373  
     75000   0.75277766     0.023186631    0.77596429     0.074859227  
     76000   0.59333539     0.024276648    0.61761204     0.076132037  
     77000   0.68243436     0.024600726    0.70703508     0.075525977  
     78000   0.79699751     0.024238959    0.82123647     0.078255526  
     79000   0.77318109     0.024249895    0.79743099     0.078223339  
     80000   0.72004911     0.024522473    0.74457159     0.079009398  
     81000   0.71732947     0.024702988    0.74203245     0.080902007  
     82000   0.73395391     0.024817681    0.75877159     0.081203115  
     83000   0.74389794     0.02487774     0.76877568     0.082273058  
     84000   0.73219737     0.024967311    0.75716468     0.08359401   
     85000   0.66523255     0.025299293    0.69053184     0.084260931  
     86000   0.67031201     0.02564609     0.6959581      0.085495986  
     87000   0.81345283     0.025297963    0.8387508      0.086292085  
     88000   0.85008513     0.024879647    0.87496478     0.087116741  
     89000   0.62893149     0.025674927    0.65460642     0.088514693  
     90000   0.58336052     0.026632218    0.60999274     0.089459637  
     91000   0.72615388     0.026181899    0.75233578     0.090289473  
     92000   0.76593408     0.025893082    0.79182717     0.091294308  
     93000   0.73475998     0.026113022    0.76087301     0.092256366  
     94000   0.68995562     0.026409704    0.71636532     0.093332419  
     95000   0.69491284     0.026726159    0.721639       0.094314615  
     96000   0.83274635     0.026420125    0.85916648     0.09513317   
     97000   0.85486073     0.025941089    0.88080181     0.096122793  
     98000   0.63095894     0.027021709    0.65798064     0.097348373  
     99000   0.60847495     0.027908563    0.63638351     0.098362493  
    100000   0.75867487     0.027331375    0.78600625     0.099184572  
Loop time of 3.87848 on 1 procs for 100000 steps with 32 atoms

Performance: 2227674.150 tau/day, 25783.266 timesteps/s, 825.065 katom-step/s
97.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.9048     | 2.9048     | 2.9048     |   0.0 | 74.90
Neigh   | 0.0027304  | 0.0027304  | 0.0027304  |   0.0 |  0.07
Comm    | 0.071653   | 0.071653   | 0.071653   |   0.0 |  1.85
Output  | 0.00069287 | 0.00069287 | 0.00069287 |   0.0 |  0.02
Modify  | 0.85771    | 0.85771    | 0.85771    |   0.0 | 22.11
Other   |            | 0.04088    |            |       |  1.05

Nlocal:             32 ave          32 max          32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             32 ave          32 max          32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:             57 ave          57 max          57 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 57
Ave neighs/atom = 1.78125
Neighbor list builds = 1379
Dangerous builds = 0
Total wall time: 0:00:03
